src/jalview/gui/PopupMenu.java

   1 /*\r
   2  * Jalview - A Sequence Alignment Editor and Viewer\r
   3  * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
   4  *\r
   5  * This program is free software; you can redistribute it and/or\r
   6  * modify it under the terms of the GNU General Public License\r
   7  * as published by the Free Software Foundation; either version 2\r
   8  * of the License, or (at your option) any later version.\r
   9  *\r
  10  * This program is distributed in the hope that it will be useful,\r
  11  * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
  12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
  13  * GNU General Public License for more details.\r
  14  *\r
  15  * You should have received a copy of the GNU General Public License\r
  16  * along with this program; if not, write to the Free Software\r
  17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
  18  */\r
  19 package jalview.gui;\r
  20 \r
  21 import MCview.*;\r
  22 \r
  23 import jalview.analysis.*;\r
  24 \r
  25 import jalview.datamodel.*;\r
  26 \r
  27 \r
  28 import jalview.schemes.*;\r
  29 \r
  30 import java.awt.*;\r
  31 import java.awt.event.*;\r
  32 \r
  33 import javax.swing.*;\r
  34 \r
  35 \r
  36 /**\r
  37  * DOCUMENT ME!\r
  38  *\r
  39  * @author $author$\r
  40  * @version $Revision$\r
  41  */\r
  42 public class PopupMenu extends JPopupMenu\r
  43 {\r
  44     JMenu groupMenu = new JMenu();\r
  45     JMenuItem groupName = new JMenuItem();\r
  46     protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();\r
  47     protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();\r
  48     protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();\r
  49     protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();\r
  50     protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();\r
  51     protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();\r
  52     protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();\r
  53     protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();\r
  54     protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();\r
  55     protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();\r
  56     protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();\r
  57     protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();\r
  58     JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();\r
  59     protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();\r
  60     AlignmentPanel ap;\r
  61     JMenu sequenceMenu = new JMenu();\r
  62     JMenuItem sequenceName = new JMenuItem();\r
  63     Sequence sequence;\r
  64     JMenuItem unGroupMenuItem = new JMenuItem();\r
  65     JMenuItem outline = new JMenuItem();\r
  66     JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();\r
  67     JMenu colourMenu = new JMenu();\r
  68     JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();\r
  69     JCheckBoxMenuItem showText = new JCheckBoxMenuItem();\r
  70     JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();\r
  71   JMenu jMenu1 = new JMenu();\r
  72   JMenuItem cut = new JMenuItem();\r
  73   JMenuItem copy = new JMenuItem();\r
  74   JMenuItem upperCase = new JMenuItem();\r
  75   JMenuItem lowerCase = new JMenuItem();\r
  76 \r
  77   /**\r
  78      * Creates a new PopupMenu object.\r
  79      *\r
  80      * @param ap DOCUMENT ME!\r
  81      * @param seq DOCUMENT ME!\r
  82      */\r
  83     public PopupMenu(final AlignmentPanel ap, Sequence seq)\r
  84     {\r
  85         ///////////////////////////////////////////////////////////\r
  86         // If this is activated from the sequence panel, the user may want to\r
  87         // edit or annotate a particular residue. Therefore display the residue menu\r
  88         //\r
  89         // If from the IDPanel, we must display the sequence menu\r
  90         //////////////////////////////////////////////////////////\r
  91         this.ap = ap;\r
  92         sequence = seq;\r
  93 \r
  94         ButtonGroup colours = new ButtonGroup();\r
  95         colours.add(noColourmenuItem);\r
  96         colours.add(clustalColour);\r
  97         colours.add(zappoColour);\r
  98         colours.add(taylorColour);\r
  99         colours.add(hydrophobicityColour);\r
 100         colours.add(helixColour);\r
 101         colours.add(strandColour);\r
 102         colours.add(turnColour);\r
 103         colours.add(buriedColour);\r
 104         colours.add(abovePIDColour);\r
 105         colours.add(userDefinedColour);\r
 106         colours.add(PIDColour);\r
 107         colours.add(BLOSUM62Colour);\r
 108 \r
 109         try\r
 110         {\r
 111             jbInit();\r
 112         }\r
 113         catch (Exception e)\r
 114         {\r
 115             e.printStackTrace();\r
 116         }\r
 117 \r
 118 \r
 119         if (seq != null)\r
 120         {\r
 121           JMenuItem menuItem;\r
 122           if( seq.getDatasetSequence().getPDBId() != null)\r
 123           {\r
 124             java.util.Enumeration e = seq.getDatasetSequence().getPDBId().\r
 125                 elements();\r
 126             while (e.hasMoreElements())\r
 127             {\r
 128               final PDBEntry pdb = (PDBEntry) e.nextElement();\r
 129 \r
 130               menuItem = new JMenuItem();\r
 131               menuItem.setText("View PDB entry: " + pdb.getId());\r
 132               menuItem.addActionListener(new java.awt.event.ActionListener()\r
 133               {\r
 134                 public void actionPerformed(ActionEvent e)\r
 135                 {\r
 136                   new PDBViewer(pdb, sequence, ap.seqPanel.seqCanvas);\r
 137                 }\r
 138               });\r
 139               sequenceMenu.add(menuItem);\r
 140             }\r
 141           }\r
 142 \r
 143        /*   menuItem = new JMenuItem("Hide Sequences");\r
 144           menuItem.addActionListener(new java.awt.event.ActionListener()\r
 145               {\r
 146                 public void actionPerformed(ActionEvent e)\r
 147                 {\r
 148                   hideSequences(false);\r
 149                 }\r
 150               });\r
 151           sequenceMenu.add(menuItem);\r
 152 \r
 153           if(ap.av.getSelectionGroup() !=null && ap.av.getSelectionGroup().getSize()>1)\r
 154           {\r
 155             menuItem = new JMenuItem("Represent Group with " + seq.getName());\r
 156             menuItem.addActionListener(new java.awt.event.ActionListener()\r
 157             {\r
 158               public void actionPerformed(ActionEvent e)\r
 159               {\r
 160                 hideSequences(true);\r
 161               }\r
 162             });\r
 163             sequenceMenu.add(menuItem);\r
 164           }*/\r
 165 \r
 166 \r
 167         }\r
 168 \r
 169 \r
 170 \r
 171         SequenceGroup sg = ap.av.getSelectionGroup();\r
 172 \r
 173         if (sg != null)\r
 174         {\r
 175             groupName.setText(sg.getName());\r
 176 \r
 177             if (sg.cs instanceof ZappoColourScheme)\r
 178             {\r
 179                 zappoColour.setSelected(true);\r
 180             }\r
 181             else if (sg.cs instanceof TaylorColourScheme)\r
 182             {\r
 183                 taylorColour.setSelected(true);\r
 184             }\r
 185             else if (sg.cs instanceof PIDColourScheme)\r
 186             {\r
 187                 PIDColour.setSelected(true);\r
 188             }\r
 189             else if (sg.cs instanceof Blosum62ColourScheme)\r
 190             {\r
 191                 BLOSUM62Colour.setSelected(true);\r
 192             }\r
 193             else if (sg.cs instanceof UserColourScheme)\r
 194             {\r
 195                 userDefinedColour.setSelected(true);\r
 196             }\r
 197             else if (sg.cs instanceof HydrophobicColourScheme)\r
 198             {\r
 199                 hydrophobicityColour.setSelected(true);\r
 200             }\r
 201             else if (sg.cs instanceof HelixColourScheme)\r
 202             {\r
 203                 helixColour.setSelected(true);\r
 204             }\r
 205             else if (sg.cs instanceof StrandColourScheme)\r
 206             {\r
 207                 strandColour.setSelected(true);\r
 208             }\r
 209             else if (sg.cs instanceof TurnColourScheme)\r
 210             {\r
 211                 turnColour.setSelected(true);\r
 212             }\r
 213             else if (sg.cs instanceof BuriedColourScheme)\r
 214             {\r
 215                 buriedColour.setSelected(true);\r
 216             }\r
 217             else if (sg.cs instanceof ClustalxColourScheme)\r
 218             {\r
 219                 clustalColour.setSelected(true);\r
 220             }\r
 221             else\r
 222             {\r
 223                 noColourmenuItem.setSelected(true);\r
 224             }\r
 225 \r
 226             if (sg.cs!=null && sg.cs.conservationApplied())\r
 227             {\r
 228                 conservationMenuItem.setSelected(true);\r
 229             }\r
 230 \r
 231             showText.setSelected(sg.getDisplayText());\r
 232             showColourText.setSelected(sg.getColourText());\r
 233             showBoxes.setSelected(sg.getDisplayBoxes());\r
 234         }\r
 235         else\r
 236           groupMenu.setVisible(false);\r
 237 \r
 238         if (!ap.av.alignment.getGroups().contains(sg))\r
 239         {\r
 240             unGroupMenuItem.setVisible(false);\r
 241         }\r
 242         else\r
 243         {\r
 244             groupMenu.insertSeparator(3);\r
 245         }\r
 246 \r
 247         if (seq == null)\r
 248         {\r
 249             sequenceMenu.setVisible(false);\r
 250         }\r
 251         else\r
 252         {\r
 253           java.util.Vector links = Preferences.sequenceURLLinks;\r
 254 \r
 255           JMenu linkMenu = new JMenu("Link");\r
 256           JMenuItem item;\r
 257           for(int i=0; i<links.size(); i++)\r
 258           {\r
 259             String link = links.elementAt(i).toString();\r
 260 \r
 261             item = new JMenuItem(link.substring(0, link.indexOf("|")));\r
 262             String id = sequence.getName();\r
 263             if(id.indexOf("|")>-1)\r
 264               id = id.substring(id.lastIndexOf("|")+1);\r
 265 \r
 266             final String url = link.substring(link.indexOf("|")+1, link.indexOf("$SEQUENCE_ID$"))\r
 267                 + id +\r
 268                 link.substring(link.indexOf("$SEQUENCE_ID$") + 13);\r
 269 \r
 270 \r
 271             item.addActionListener(new java.awt.event.ActionListener()\r
 272             {\r
 273                 public void actionPerformed(ActionEvent e)\r
 274                 {\r
 275                     showLink(url);\r
 276                 }\r
 277             });\r
 278 \r
 279             linkMenu.add(item);\r
 280           }\r
 281           add(linkMenu);\r
 282         }\r
 283     }\r
 284 \r
 285 \r
 286     /**\r
 287      * DOCUMENT ME!\r
 288      *\r
 289      * @throws Exception DOCUMENT ME!\r
 290      */\r
 291     private void jbInit() throws Exception\r
 292     {\r
 293         groupMenu.setText("Group");\r
 294         groupMenu.setText("Group");\r
 295         groupName.setText("Name");\r
 296         groupName.addActionListener(new java.awt.event.ActionListener()\r
 297             {\r
 298                 public void actionPerformed(ActionEvent e)\r
 299                 {\r
 300                     groupName_actionPerformed(e);\r
 301                 }\r
 302             });\r
 303         sequenceMenu.setText("Sequence");\r
 304         sequenceName.setText("Edit Name/Description");\r
 305         sequenceName.addActionListener(new java.awt.event.ActionListener()\r
 306             {\r
 307                 public void actionPerformed(ActionEvent e)\r
 308                 {\r
 309                     sequenceName_actionPerformed(e);\r
 310                 }\r
 311             });\r
 312         PIDColour.setFocusPainted(false);\r
 313         unGroupMenuItem.setText("Remove Group");\r
 314         unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 315             {\r
 316                 public void actionPerformed(ActionEvent e)\r
 317                 {\r
 318                     unGroupMenuItem_actionPerformed(e);\r
 319                 }\r
 320             });\r
 321 \r
 322         outline.setText("Border colour");\r
 323         outline.addActionListener(new java.awt.event.ActionListener()\r
 324             {\r
 325                 public void actionPerformed(ActionEvent e)\r
 326                 {\r
 327                     outline_actionPerformed(e);\r
 328                 }\r
 329             });\r
 330         nucleotideMenuItem.setText("Nucleotide");\r
 331         nucleotideMenuItem.addActionListener(new ActionListener()\r
 332             {\r
 333                 public void actionPerformed(ActionEvent e)\r
 334                 {\r
 335                     nucleotideMenuItem_actionPerformed(e);\r
 336                 }\r
 337             });\r
 338         colourMenu.setText("Group Colour");\r
 339         showBoxes.setText("Boxes");\r
 340         showBoxes.setState(true);\r
 341         showBoxes.addActionListener(new ActionListener()\r
 342             {\r
 343                 public void actionPerformed(ActionEvent e)\r
 344                 {\r
 345                     showBoxes_actionPerformed(e);\r
 346                 }\r
 347             });\r
 348         showText.setText("Text");\r
 349         showText.setState(true);\r
 350         showText.addActionListener(new ActionListener()\r
 351             {\r
 352                 public void actionPerformed(ActionEvent e)\r
 353                 {\r
 354                     showText_actionPerformed(e);\r
 355                 }\r
 356             });\r
 357         showColourText.setText("Colour Text");\r
 358         showColourText.addActionListener(new ActionListener()\r
 359             {\r
 360                 public void actionPerformed(ActionEvent e)\r
 361                 {\r
 362                     showColourText_actionPerformed(e);\r
 363                 }\r
 364             });\r
 365     jMenu1.setText("Edit");\r
 366     cut.setText("Cut");\r
 367     cut.addActionListener(new ActionListener()\r
 368     {\r
 369       public void actionPerformed(ActionEvent e)\r
 370       {\r
 371         cut_actionPerformed(e);\r
 372       }\r
 373     });\r
 374     upperCase.setText("To Upper Case");\r
 375     upperCase.addActionListener(new ActionListener()\r
 376     {\r
 377       public void actionPerformed(ActionEvent e)\r
 378       {\r
 379         upperCase_actionPerformed(e);\r
 380       }\r
 381     });\r
 382     copy.setText("Copy");\r
 383     copy.addActionListener(new ActionListener()\r
 384     {\r
 385       public void actionPerformed(ActionEvent e)\r
 386       {\r
 387         copy_actionPerformed(e);\r
 388       }\r
 389     });\r
 390     lowerCase.setText("To Lower Case");\r
 391     lowerCase.addActionListener(new ActionListener()\r
 392     {\r
 393       public void actionPerformed(ActionEvent e)\r
 394       {\r
 395         lowerCase_actionPerformed(e);\r
 396       }\r
 397     });\r
 398     add(groupMenu);\r
 399         add(sequenceMenu);\r
 400     this.add(jMenu1);\r
 401     groupMenu.add(groupName);\r
 402         groupMenu.addSeparator();\r
 403         groupMenu.add(unGroupMenuItem);\r
 404         groupMenu.add(colourMenu);\r
 405         groupMenu.addSeparator();\r
 406         groupMenu.add(showBoxes);\r
 407         groupMenu.add(showText);\r
 408         groupMenu.add(showColourText);\r
 409         groupMenu.addSeparator();\r
 410         groupMenu.add(outline);\r
 411         sequenceMenu.add(sequenceName);\r
 412         colourMenu.add(noColourmenuItem);\r
 413         colourMenu.add(clustalColour);\r
 414         colourMenu.add(BLOSUM62Colour);\r
 415         colourMenu.add(PIDColour);\r
 416         colourMenu.add(zappoColour);\r
 417         colourMenu.add(taylorColour);\r
 418         colourMenu.add(hydrophobicityColour);\r
 419         colourMenu.add(helixColour);\r
 420         colourMenu.add(strandColour);\r
 421         colourMenu.add(turnColour);\r
 422         colourMenu.add(buriedColour);\r
 423         colourMenu.add(nucleotideMenuItem);\r
 424         colourMenu.add(userDefinedColour);\r
 425 \r
 426         if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)\r
 427         {\r
 428           java.util.Enumeration userColours = jalview.gui.UserDefinedColours.\r
 429               getUserColourSchemes().keys();\r
 430 \r
 431           while (userColours.hasMoreElements())\r
 432           {\r
 433             JMenuItem item = new JMenuItem(userColours.\r
 434                 nextElement().toString());\r
 435             item.addActionListener(new ActionListener()\r
 436             {\r
 437               public void actionPerformed(ActionEvent evt)\r
 438               {\r
 439                 userDefinedColour_actionPerformed(evt);\r
 440               }\r
 441             });\r
 442             colourMenu.add(item);\r
 443           }\r
 444         }\r
 445 \r
 446 \r
 447         colourMenu.addSeparator();\r
 448         colourMenu.add(abovePIDColour);\r
 449         colourMenu.add(conservationMenuItem);\r
 450     jMenu1.add(copy);\r
 451     jMenu1.add(cut);\r
 452     jMenu1.add(upperCase);\r
 453     jMenu1.add(lowerCase);\r
 454     noColourmenuItem.setText("None");\r
 455         noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
 456             {\r
 457                 public void actionPerformed(ActionEvent e)\r
 458                 {\r
 459                     noColourmenuItem_actionPerformed(e);\r
 460                 }\r
 461             });\r
 462 \r
 463         clustalColour.setText("Clustalx colours");\r
 464         clustalColour.addActionListener(new java.awt.event.ActionListener()\r
 465             {\r
 466                 public void actionPerformed(ActionEvent e)\r
 467                 {\r
 468                     clustalColour_actionPerformed(e);\r
 469                 }\r
 470             });\r
 471         zappoColour.setText("Zappo");\r
 472         zappoColour.addActionListener(new java.awt.event.ActionListener()\r
 473             {\r
 474                 public void actionPerformed(ActionEvent e)\r
 475                 {\r
 476                     zappoColour_actionPerformed(e);\r
 477                 }\r
 478             });\r
 479         taylorColour.setText("Taylor");\r
 480         taylorColour.addActionListener(new java.awt.event.ActionListener()\r
 481             {\r
 482                 public void actionPerformed(ActionEvent e)\r
 483                 {\r
 484                     taylorColour_actionPerformed(e);\r
 485                 }\r
 486             });\r
 487         hydrophobicityColour.setText("Hydrophobicity");\r
 488         hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
 489             {\r
 490                 public void actionPerformed(ActionEvent e)\r
 491                 {\r
 492                     hydrophobicityColour_actionPerformed(e);\r
 493                 }\r
 494             });\r
 495         helixColour.setText("Helix propensity");\r
 496         helixColour.addActionListener(new java.awt.event.ActionListener()\r
 497             {\r
 498                 public void actionPerformed(ActionEvent e)\r
 499                 {\r
 500                     helixColour_actionPerformed(e);\r
 501                 }\r
 502             });\r
 503         strandColour.setText("Strand propensity");\r
 504         strandColour.addActionListener(new java.awt.event.ActionListener()\r
 505             {\r
 506                 public void actionPerformed(ActionEvent e)\r
 507                 {\r
 508                     strandColour_actionPerformed(e);\r
 509                 }\r
 510             });\r
 511         turnColour.setText("Turn propensity");\r
 512         turnColour.addActionListener(new java.awt.event.ActionListener()\r
 513             {\r
 514                 public void actionPerformed(ActionEvent e)\r
 515                 {\r
 516                     turnColour_actionPerformed(e);\r
 517                 }\r
 518             });\r
 519         buriedColour.setText("Buried Index");\r
 520         buriedColour.addActionListener(new java.awt.event.ActionListener()\r
 521             {\r
 522                 public void actionPerformed(ActionEvent e)\r
 523                 {\r
 524                     buriedColour_actionPerformed(e);\r
 525                 }\r
 526             });\r
 527         abovePIDColour.setText("Above % Identity");\r
 528         abovePIDColour.addActionListener(new java.awt.event.ActionListener()\r
 529             {\r
 530                 public void actionPerformed(ActionEvent e)\r
 531                 {\r
 532                     abovePIDColour_actionPerformed(e);\r
 533                 }\r
 534             });\r
 535         userDefinedColour.setText("User Defined...");\r
 536         userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
 537             {\r
 538                 public void actionPerformed(ActionEvent e)\r
 539                 {\r
 540                     userDefinedColour_actionPerformed(e);\r
 541                 }\r
 542             });\r
 543         PIDColour.setText("Percentage Identity");\r
 544         PIDColour.addActionListener(new java.awt.event.ActionListener()\r
 545             {\r
 546                 public void actionPerformed(ActionEvent e)\r
 547                 {\r
 548                     PIDColour_actionPerformed(e);\r
 549                 }\r
 550             });\r
 551         BLOSUM62Colour.setText("BLOSUM62");\r
 552         BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
 553             {\r
 554                 public void actionPerformed(ActionEvent e)\r
 555                 {\r
 556                     BLOSUM62Colour_actionPerformed(e);\r
 557                 }\r
 558             });\r
 559         conservationMenuItem.setText("Conservation");\r
 560         conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 561             {\r
 562                 public void actionPerformed(ActionEvent e)\r
 563                 {\r
 564                     conservationMenuItem_actionPerformed(e);\r
 565                 }\r
 566             });\r
 567     }\r
 568 \r
 569     /**\r
 570      * DOCUMENT ME!\r
 571      */\r
 572     void refresh()\r
 573     {\r
 574         if (ap.overviewPanel != null)\r
 575           ap.overviewPanel.updateOverviewImage();\r
 576 \r
 577         ap.seqPanel.repaint();\r
 578     }\r
 579 \r
 580     /**\r
 581      * DOCUMENT ME!\r
 582      *\r
 583      * @param e DOCUMENT ME!\r
 584      */\r
 585     protected void clustalColour_actionPerformed(ActionEvent e)\r
 586     {\r
 587         SequenceGroup sg = getGroup();\r
 588         sg.cs = new ClustalxColourScheme(sg.sequences,\r
 589                 ap.av.alignment.getWidth());\r
 590         refresh();\r
 591     }\r
 592 \r
 593     /**\r
 594      * DOCUMENT ME!\r
 595      *\r
 596      * @param e DOCUMENT ME!\r
 597      */\r
 598     protected void zappoColour_actionPerformed(ActionEvent e)\r
 599     {\r
 600         getGroup().cs = new ZappoColourScheme();\r
 601         refresh();\r
 602     }\r
 603 \r
 604     /**\r
 605      * DOCUMENT ME!\r
 606      *\r
 607      * @param e DOCUMENT ME!\r
 608      */\r
 609     protected void taylorColour_actionPerformed(ActionEvent e)\r
 610     {\r
 611         getGroup().cs = new TaylorColourScheme();\r
 612         refresh();\r
 613     }\r
 614 \r
 615     /**\r
 616      * DOCUMENT ME!\r
 617      *\r
 618      * @param e DOCUMENT ME!\r
 619      */\r
 620     protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 621     {\r
 622         getGroup().cs = new HydrophobicColourScheme();\r
 623         refresh();\r
 624     }\r
 625 \r
 626     /**\r
 627      * DOCUMENT ME!\r
 628      *\r
 629      * @param e DOCUMENT ME!\r
 630      */\r
 631     protected void helixColour_actionPerformed(ActionEvent e)\r
 632     {\r
 633         getGroup().cs = new HelixColourScheme();\r
 634         refresh();\r
 635     }\r
 636 \r
 637     /**\r
 638      * DOCUMENT ME!\r
 639      *\r
 640      * @param e DOCUMENT ME!\r
 641      */\r
 642     protected void strandColour_actionPerformed(ActionEvent e)\r
 643     {\r
 644         getGroup().cs = new StrandColourScheme();\r
 645         refresh();\r
 646     }\r
 647 \r
 648     /**\r
 649      * DOCUMENT ME!\r
 650      *\r
 651      * @param e DOCUMENT ME!\r
 652      */\r
 653     protected void turnColour_actionPerformed(ActionEvent e)\r
 654     {\r
 655         getGroup().cs = new TurnColourScheme();\r
 656         refresh();\r
 657     }\r
 658 \r
 659     /**\r
 660      * DOCUMENT ME!\r
 661      *\r
 662      * @param e DOCUMENT ME!\r
 663      */\r
 664     protected void buriedColour_actionPerformed(ActionEvent e)\r
 665     {\r
 666         getGroup().cs = new BuriedColourScheme();\r
 667         refresh();\r
 668     }\r
 669 \r
 670     /**\r
 671      * DOCUMENT ME!\r
 672      *\r
 673      * @param e DOCUMENT ME!\r
 674      */\r
 675     public void nucleotideMenuItem_actionPerformed(ActionEvent e)\r
 676     {\r
 677         getGroup().cs = new NucleotideColourScheme();\r
 678         refresh();\r
 679     }\r
 680 \r
 681     /**\r
 682      * DOCUMENT ME!\r
 683      *\r
 684      * @param e DOCUMENT ME!\r
 685      */\r
 686     protected void abovePIDColour_actionPerformed(ActionEvent e)\r
 687     {\r
 688         SequenceGroup sg = getGroup();\r
 689         if(sg.cs==null)\r
 690           return;\r
 691 \r
 692         if (abovePIDColour.isSelected())\r
 693         {\r
 694             sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
 695                     ap.av.alignment.getWidth()));\r
 696 \r
 697             int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,\r
 698                     getGroup().getName());\r
 699 \r
 700            sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());\r
 701 \r
 702             SliderPanel.showPIDSlider();\r
 703         }\r
 704         else // remove PIDColouring\r
 705         {\r
 706             sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());\r
 707         }\r
 708 \r
 709         refresh();\r
 710     }\r
 711 \r
 712     /**\r
 713      * DOCUMENT ME!\r
 714      *\r
 715      * @param e DOCUMENT ME!\r
 716      */\r
 717     protected void userDefinedColour_actionPerformed(ActionEvent e)\r
 718     {\r
 719        SequenceGroup sg = getGroup();\r
 720 \r
 721        if (e.getActionCommand().equals("User Defined..."))\r
 722          new UserDefinedColours(ap, sg);\r
 723        else\r
 724        {\r
 725          UserColourScheme udc = (UserColourScheme) UserDefinedColours.\r
 726              getUserColourSchemes().get(e.getActionCommand());\r
 727 \r
 728          sg.cs = udc;\r
 729        }\r
 730      }\r
 731     /**\r
 732      * DOCUMENT ME!\r
 733      *\r
 734      * @param e DOCUMENT ME!\r
 735      */\r
 736     protected void PIDColour_actionPerformed(ActionEvent e)\r
 737     {\r
 738         SequenceGroup sg = getGroup();\r
 739         sg.cs = new PIDColourScheme();\r
 740         sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
 741                 ap.av.alignment.getWidth()));\r
 742         refresh();\r
 743     }\r
 744 \r
 745     /**\r
 746      * DOCUMENT ME!\r
 747      *\r
 748      * @param e DOCUMENT ME!\r
 749      */\r
 750     protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 751     {\r
 752         SequenceGroup sg = getGroup();\r
 753 \r
 754         sg.cs = new Blosum62ColourScheme();\r
 755 \r
 756         sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
 757                 ap.av.alignment.getWidth()));\r
 758 \r
 759         refresh();\r
 760     }\r
 761 \r
 762     /**\r
 763      * DOCUMENT ME!\r
 764      *\r
 765      * @param e DOCUMENT ME!\r
 766      */\r
 767     protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 768     {\r
 769         getGroup().cs = null;\r
 770         refresh();\r
 771     }\r
 772 \r
 773     /**\r
 774      * DOCUMENT ME!\r
 775      *\r
 776      * @param e DOCUMENT ME!\r
 777      */\r
 778     protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
 779     {\r
 780         SequenceGroup sg = getGroup();\r
 781         if(sg.cs==null)\r
 782           return;\r
 783 \r
 784         if (conservationMenuItem.isSelected())\r
 785         {\r
 786             Conservation c = new Conservation("Group",\r
 787                     ResidueProperties.propHash, 3, sg.sequences, 0,\r
 788                     ap.av.alignment.getWidth());\r
 789 \r
 790             c.calculate();\r
 791             c.verdict(false, ap.av.ConsPercGaps);\r
 792 \r
 793             sg.cs.setConservation(c);\r
 794 \r
 795             SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());\r
 796             SliderPanel.showConservationSlider();\r
 797         }\r
 798         else // remove ConservationColouring\r
 799         {\r
 800             sg.cs.setConservation(null);\r
 801         }\r
 802 \r
 803         refresh();\r
 804     }\r
 805 \r
 806     /**\r
 807      * DOCUMENT ME!\r
 808      *\r
 809      * @param e DOCUMENT ME!\r
 810      */\r
 811     protected void groupName_actionPerformed(ActionEvent e)\r
 812     {\r
 813         SequenceGroup sg = getGroup();\r
 814         String reply = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
 815                 "Enter new group name", "Edit group name",\r
 816                 JOptionPane.QUESTION_MESSAGE);\r
 817 \r
 818         if (reply == null)\r
 819         {\r
 820             return;\r
 821         }\r
 822 \r
 823         sg.setName(reply);\r
 824         groupName.setText(reply);\r
 825     }\r
 826 \r
 827     /**\r
 828      * DOCUMENT ME!\r
 829      *\r
 830      * @param e DOCUMENT ME!\r
 831      */\r
 832     protected void analyze_actionPerformed(ActionEvent e)\r
 833     {\r
 834         CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
 835         JInternalFrame frame = new JInternalFrame();\r
 836         frame.setContentPane(cap);\r
 837         Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);\r
 838 \r
 839         SequenceGroup sg = getGroup();\r
 840         StringBuffer sb = new StringBuffer();\r
 841 \r
 842         for (int i = 0; i < sg.sequences.size(); i++)\r
 843         {\r
 844             Sequence tmp = (Sequence) sg.sequences.get(i);\r
 845             sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1));\r
 846             sb.append("\n");\r
 847         }\r
 848 \r
 849         sb.append("Something amazing will happen soon");\r
 850         cap.setText(sb.toString());\r
 851     }\r
 852 \r
 853     /**\r
 854      * DOCUMENT ME!\r
 855      *\r
 856      * @return DOCUMENT ME!\r
 857      */\r
 858     SequenceGroup getGroup()\r
 859     {\r
 860         SequenceGroup sg = ap.av.getSelectionGroup();\r
 861       // this method won't add a new group if it already exists\r
 862         if(sg!=null)\r
 863           ap.av.alignment.addGroup(sg);\r
 864 \r
 865         return sg;\r
 866     }\r
 867 \r
 868     /**\r
 869      * DOCUMENT ME!\r
 870      *\r
 871      * @param e DOCUMENT ME!\r
 872      */\r
 873     void sequenceName_actionPerformed(ActionEvent e)\r
 874     {\r
 875       JLabel idlabel = new JLabel(  "       Sequence Name ");\r
 876       JLabel desclabel = new JLabel("Sequence Description ");\r
 877       idlabel.setFont(new Font("Courier", Font.PLAIN, 12));\r
 878       desclabel.setFont(new Font("Courier", Font.PLAIN, 12));\r
 879       JTextField id = new JTextField(sequence.getName(), 40);\r
 880       JTextField description = new JTextField(sequence.getDescription(), 40);\r
 881       JPanel panel = new JPanel(new BorderLayout());\r
 882       JPanel panel2 = new JPanel(new BorderLayout());\r
 883       panel2.add(idlabel, BorderLayout.WEST);\r
 884       panel2.add(id, BorderLayout.CENTER);\r
 885       panel.add(panel2, BorderLayout.NORTH);\r
 886       panel2 = new JPanel(new BorderLayout());\r
 887       panel2.add(desclabel, BorderLayout.WEST);\r
 888       panel2.add(description, BorderLayout.CENTER);\r
 889       panel.add(panel2, BorderLayout.SOUTH);\r
 890 \r
 891 \r
 892        int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,\r
 893           panel, "Edit Sequence Name/Description",\r
 894           JOptionPane.OK_CANCEL_OPTION );\r
 895 \r
 896 \r
 897         if (reply != JOptionPane.OK_OPTION )\r
 898         {\r
 899             return;\r
 900         }\r
 901 \r
 902         String s = id.getText();\r
 903 \r
 904         if (s != null)\r
 905         {\r
 906             if (s.indexOf(" ") > -1)\r
 907             {\r
 908                 JOptionPane.showMessageDialog(ap,\r
 909                     "Spaces have been converted to \"_\"",\r
 910                     "No spaces allowed in Sequence Name",\r
 911                     JOptionPane.WARNING_MESSAGE);\r
 912             }\r
 913 \r
 914             s = s.replace(' ', '_');\r
 915             sequence.getDatasetSequence().setName(s);\r
 916             sequence.setName(s);\r
 917             ap.repaint();\r
 918         }\r
 919 \r
 920         sequence.getDatasetSequence().setDescription(description.getText());\r
 921         sequence.setDescription(description.getText());\r
 922     }\r
 923 \r
 924     /**\r
 925      * DOCUMENT ME!\r
 926      *\r
 927      * @param e DOCUMENT ME!\r
 928      */\r
 929     void unGroupMenuItem_actionPerformed(ActionEvent e)\r
 930     {\r
 931         SequenceGroup sg = ap.av.getSelectionGroup();\r
 932         ap.av.alignment.deleteGroup(sg);\r
 933         ap.av.setSelectionGroup(null);\r
 934         refresh();\r
 935     }\r
 936 \r
 937 \r
 938     /**\r
 939      * DOCUMENT ME!\r
 940      *\r
 941      * @param e DOCUMENT ME!\r
 942      */\r
 943     protected void outline_actionPerformed(ActionEvent e)\r
 944     {\r
 945         SequenceGroup sg = getGroup();\r
 946         Color col = JColorChooser.showDialog(this, "Select Outline Colour",\r
 947                 Color.BLUE);\r
 948 \r
 949         if (col != null)\r
 950         {\r
 951             sg.setOutlineColour(col);\r
 952         }\r
 953 \r
 954         refresh();\r
 955     }\r
 956 \r
 957     /**\r
 958      * DOCUMENT ME!\r
 959      *\r
 960      * @param e DOCUMENT ME!\r
 961      */\r
 962     public void showBoxes_actionPerformed(ActionEvent e)\r
 963     {\r
 964         getGroup().setDisplayBoxes(showBoxes.isSelected());\r
 965         refresh();\r
 966     }\r
 967 \r
 968     /**\r
 969      * DOCUMENT ME!\r
 970      *\r
 971      * @param e DOCUMENT ME!\r
 972      */\r
 973     public void showText_actionPerformed(ActionEvent e)\r
 974     {\r
 975         getGroup().setDisplayText(showText.isSelected());\r
 976         refresh();\r
 977     }\r
 978 \r
 979     /**\r
 980      * DOCUMENT ME!\r
 981      *\r
 982      * @param e DOCUMENT ME!\r
 983      */\r
 984     public void showColourText_actionPerformed(ActionEvent e)\r
 985     {\r
 986         getGroup().setColourText(showColourText.isSelected());\r
 987         refresh();\r
 988     }\r
 989 \r
 990     public void showLink(String url)\r
 991     {\r
 992       try\r
 993       {\r
 994         jalview.util.BrowserLauncher.openURL(url);\r
 995       }\r
 996       catch (Exception ex)\r
 997       {\r
 998         JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
 999             "Unixers: Couldn't find default web browser."\r
1000            +"\nAdd the full path to your browser in Preferences.",\r
1001            "Web browser not found", JOptionPane.WARNING_MESSAGE );\r
1002 \r
1003 \r
1004         ex.printStackTrace();\r
1005       }\r
1006     }\r
1007 \r
1008     void hideSequences(boolean representGroup)\r
1009     {\r
1010       SequenceGroup sg = ap.av.getSelectionGroup();\r
1011       if(sg==null || sg.getSize()<1)\r
1012       {\r
1013         ap.av.hideSequence(sequence);\r
1014         return;\r
1015       }\r
1016 \r
1017         int index = 0;\r
1018         while(index < sg.sequences.size())\r
1019         {\r
1020           if(representGroup && sg.getSequenceAt(index)!=sequence)\r
1021           {\r
1022             sequence.addHiddenSequence(sg.getSequenceAt(index));\r
1023             ap.av.hideSequence(sg.getSequenceAt(index));\r
1024           }\r
1025           else if(!representGroup)\r
1026           {\r
1027             ap.av.hideSequence(sg.getSequenceAt(index));\r
1028           }\r
1029           index ++;\r
1030         }\r
1031 \r
1032         ap.av.setSelectionGroup(null);\r
1033         refresh();\r
1034     }\r
1035 \r
1036   public void copy_actionPerformed(ActionEvent e)\r
1037   {\r
1038     ap.alignFrame.copy_actionPerformed(null);\r
1039   }\r
1040 \r
1041   public void cut_actionPerformed(ActionEvent e)\r
1042   {\r
1043     ap.alignFrame.cut_actionPerformed(null);\r
1044   }\r
1045 \r
1046   public void upperCase_actionPerformed(ActionEvent e)\r
1047   {\r
1048     SequenceGroup sg = ap.av.getSelectionGroup();\r
1049     if(sg==null)\r
1050       return;\r
1051 \r
1052     for(int g=0; g<sg.getSize(); g++)\r
1053     {\r
1054       sg.getSequenceAt(g).changeCase(true, sg.getStartRes(), sg.getEndRes()+1);\r
1055     }\r
1056     ap.repaint();\r
1057   }\r
1058 \r
1059   public void lowerCase_actionPerformed(ActionEvent e)\r
1060   {\r
1061     SequenceGroup sg = ap.av.getSelectionGroup();\r
1062     if(sg==null)\r
1063       return;\r
1064 \r
1065     for(int g=0; g<sg.getSize(); g++)\r
1066     {\r
1067       sg.getSequenceAt(g).changeCase(false, sg.getStartRes(), sg.getEndRes()+1);\r
1068     }\r
1069     ap.repaint();\r
1070   }\r
1071 \r
1072 }\r